Aebersold, R. & Mann, M. Mass spectrometry-based proteomics. Nature 422, 198–207 (2003).
Article CAS PubMed Google Scholar
Smith, L. M. & Kelleher, N. L. Proteoforms as the next proteomics currency. Science 359, 1106–1107 (2018).
Article CAS PubMed PubMed Central Google Scholar
Schaffer, L. V. et al. Identification and quantification of proteoforms by mass spectrometry. Proteomics 19, e1800361 (2019).
Article PubMed PubMed Central Google Scholar
Brown, K. A., Melby, J. A., Roberts, D. S. & Ge, Y. Top-down proteomics: challenges, innovations, and applications in basic and clinical research. Expert Rev. Proteom. 17, 719–733 (2020).
Su, T., Hollas, M. A. R., Fellers, R. T. & Kelleher, N. L. Identification of splice variants and isoforms in transcriptomics and proteomics. Annu. Rev. Biomed. Data Sci. 6, 357–376 (2023).
Article PubMed PubMed Central Google Scholar
Drown, B. S. et al. Mapping the proteoform landscape of five human tissues. J. Proteome Res. 21, 1299–1310 (2022).
Article CAS PubMed PubMed Central Google Scholar
Adams, L. M. et al. Mapping the KRAS proteoform landscape in colorectal cancer identifies truncated KRAS4B that decreases MAPK signaling. J. Biol. Chem. 299, 102768 (2023).
Article CAS PubMed Google Scholar
Melani, R. D. et al. The Blood Proteoform Atlas: a reference map of proteoforms in human hematopoietic cells. Science 375, 411–418 (2022).
Article CAS PubMed PubMed Central Google Scholar
Compton, P. D., Zamdborg, L., Thomas, P. M. & Kelleher, N. L. On the scalability and requirements of whole protein mass spectrometry. Anal. Chem. 83, 6868–6874 (2011).
Article CAS PubMed PubMed Central Google Scholar
Tsiatsiani, L. & Heck, A. J. Proteomics beyond trypsin. FEBS J. 282, 2612–2626 (2015).
Article CAS PubMed Google Scholar
Sidoli, S. & Garcia, B. A. Middle-down proteomics: a still unexploited resource for chromatin biology. Expert Rev. Proteom. 14, 617–626 (2017).
Takemori, A. et al. GeLC-FAIMS-MS workflow for in-depth middle-down proteomics. Proteomics 24, e2200431 (2024).
Guo, Y., Cupp‐Sutton, K. A., Zhao, Z., Anjum, S. & Wu, S. Multidimensional separations in top–down proteomics. Anal. Sci. Adv. 4, 181–203 (2023).
Article CAS PubMed PubMed Central Google Scholar
Nickerson, J. L. et al. Recent advances in top-down proteome sample processing ahead of MS analysis. Mass Spectrom. Rev. 42, 457–495 (2023).
Article CAS PubMed Google Scholar
Laemmli, U. K. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227, 680–685 (1970).
Article CAS PubMed Google Scholar
Pflieger, D. et al. Systematic identification of mitochondrial proteins by LC-MS/MS. Anal. Chem. 74, 2400–2406 (2002).
Article CAS PubMed Google Scholar
Schirle, M., Heurtier, M. A. & Kuster, B. Profiling core proteomes of human cell lines by one-dimensional PAGE and liquid chromatography-tandem mass spectrometry. Mol. Cell. Proteom. 2, 1297–1305 (2003).
Takemori, A. et al. BAC-DROP: rapid digestion of proteome fractionated via dissolvable polyacrylamide gel electrophoresis and its application to bottom-up proteomics workflow. J. Proteome Res. 20, 1535–1543 (2021).
Article CAS PubMed Google Scholar
Takemori, A. et al. PEPPI-MS: polyacrylamide-gel-based prefractionation for analysis of intact proteoforms and protein complexes by mass spectrometry. J. Proteome Res. 19, 3779–3791 (2020).
Article CAS PubMed PubMed Central Google Scholar
Takemori, A. & Takemori, N. Sample preparation for structural mass spectrometry via polyacrylamide gel electrophoresis. Methods Enzymol. 682, 187–210 (2023).
Article CAS PubMed Google Scholar
Takemori, N. & Takemori, A. In-depth structural proteomics integrating mass spectrometry and polyacrylamide gel electrophoresis. Front. Anal. Sci. 2, 1107183 (2023).
Takemori, A., Kaulich, P. T., Cassidy, L., Takemori, N. & Tholey, A. Size-based proteome fractionation through polyacrylamide gel electrophoresis combined with LC-FAIMS-MS for in-depth top-down proteomics. Anal. Chem. 94, 12815–12821 (2022).
Article CAS PubMed Google Scholar
Le Maire, M., Deschamps, S., Møller, J. V., Le Caer, J. P. & Rossier, J. Electrospray ionization mass spectrometry on hydrophobic peptides electroeluted from sodium dodecyl sulfate-polyacrylamide gel electrophoresis application to the topology of the sarcoplasmic reticulum Ca2+ ATPase. Anal. Biochem. 214, 50–57 (1993).
Schuhmacher, M., Glocker, M. O., Wunderlin, M. & Przybylski, M. Direct isolation of proteins from sodium dodecyl sulfate-polyacrylamide gel electrophoresis and analysis by electrospray-ionization mass spectrometry. Electrophoresis 17, 848–854 (1996).
Article CAS PubMed Google Scholar
Shevchenko, A., Tomas, H., Havlis, J., Olsen, J. V. & Mann, M. In-gel digestion for mass spectrometric characterization of proteins and proteomes. Nat. Protoc. 1, 2856–2860 (2006).
Article CAS PubMed Google Scholar
Seelert, H. & Krause, F. Preparative isolation of protein complexes and other bioparticles by elution from polyacrylamide gels. Electrophoresis 29, 2617–2636 (2008).
Article CAS PubMed Google Scholar
Cohen, S. L. & Chait, B. T. Mass spectrometry of whole proteins eluted from sodium dodecyl sulfate-polyacrylamide gel electrophoresis gels. Anal. Biochem. 247, 257–267 (1997).
Article CAS PubMed Google Scholar
Claverol, S., Burlet-Schiltz, O., Gairin, J. E. & Monsarrat, B. Characterization of protein variants and post-translational modifications: ESI-MSn analyses of intact proteins eluted from polyacrylamide gels. Mol. Cell. Proteom. 2, 483–493 (2003).
Fulcher, J. M. et al. Enhancing top-down proteomics of brain tissue with FAIMS. J. Proteome Res. 20, 2780–2795 (2021).
Article CAS PubMed PubMed Central Google Scholar
Reed, B. D. et al. Real-time dynamic single-molecule protein sequencing on an integrated semiconductor device. Science 378, 186–192 (2022).
Article CAS PubMed Google Scholar
Leney, A. C. & Heck, A. J. R. Native mass spectrometry: what is in the name? J. Am. Soc. Mass Spectrom. 28, 5–13 (2017).
Article CAS PubMed Google Scholar
Zhou, M. et al. Higher-order structural characterisation of native proteins and complexes by top-down mass spectrometry. Chem. Sci. 11, 12918–12936 (2020).
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